So, I have 2 Marketo Nurture program running one of them has 5 emails and another has 3 emails. I have listed down how they should behave:

Everyone who is new to the database should be enrolled in the 5 emails (say email A, B,C D and E) Nurture program

Everyone who already exists in the database and those who received Email A and B should be enrolled in the 3 email Nurture program

I recently uploaded 30k contacts to Marketo (who are new to the database), however found out that 15k of them were enrolled in 5 email Nurture program and rest 15k in the 3 email program. It seems weird and I cannot seem to figure out why.

It would be great if you can post your "qualification smart list rules" that you have for both Nurture 1 and 2. Also screenshots of the activity for the leads that qualified for Nurture 1 and leads that qualified for Nurture 2.

As Floyd said, we would need to see the smart list criteria for your entry campaigns for both nurtures and ideally examples of activity logs for a person in each nurture.

If you're unable to share those, the first thing I would do is double check the criteria of each entry campaign to see if there are any errors in logic (something easy to miss like AND instead of OR or IS instead of IS NOT can throw everything off). If that doesn't get me anywhere, looking into the activity log can help pinpoint how a person could have qualified when they should not have (e.g. an incorrect data management campaign changed a field and allowed them to qualify early).

Just out of curiosity, what was the source of those 30k contacts? I only ask because many of us are on shared IPs and have seen an uptick of blacklisting in our monitoring service, resulting in a decrease in our overall deliverability. This often occurs when sending out unsolicited emails to purchased lists or those that haven't provided their consent. This sort of activity will impact everyone sharing those IP addresses. I'm not implying you're guilty of this behavior - just asking.

Given your situation, I would highly recommend scrutinizing the activity logs of the leads who qualified (Who were not supposed to qualify). That most certainly should get you the answer. Alternatively, Since you cannot share the Smart list screen shots or the activity log screen shots over here, After carefully scrutinizing the activity log, if you still do not find any issue, and the activity logs are telling a different story from what you have defined in the smart list, then I would recommend getting in touch with Marketo support.